1
$\begingroup$

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE.

  1. I would like to ask if consistency score plays any role in the interpretation?
  2. I would like to ask for a region of a protein to be considered conserved, all the amino acids should have similar properties? So even if only one protein has a different amino acid (among the proteins that are included in the multiple alignment), then there is no conservation? for example, in this picture,
  3. I am curious why there is no dot beneath some columns with almost identical amino acids (expect one sequence for example).enter image description here
Improve this question
$\endgroup$
4
  • $\begingroup$ Good question but we will need to know what the purpose of conservation analysis is. Make primers? State "region of conservation"? Design a vaccine? $\endgroup$
    – M__ ♦
    Commented Apr 27, 2020 at 11:37
  • 1
    $\begingroup$ the ultimate goal is to find some information about the structure and the function of an unknown protein sequence. $\endgroup$
    – marilu
    Commented Apr 27, 2020 at 18:35
  • $\begingroup$ Thanks I'll respond in a few days, my apologies for the delay in advance. $\endgroup$
    – M__ ♦
    Commented Apr 27, 2020 at 18:48
  • $\begingroup$ no worries!thank you so much for your help!i am grateful! $\endgroup$
    – marilu
    Commented Apr 27, 2020 at 19:00

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.